Added support for Tax2Tree to align_seqs.py
Rearranged/renamed files to be more functional
Messed up the rm command in the last commit.
Large changes to the interface, code, and capabilities of compare_alpha_diversities.py. Addresses issue #498 as well as a bug fix for multiple comparisons.
Removed print statements and updated documentation.
some documentation updates. this addresses #518
Changed docstring to be more accurate. Updated ChangeLog
Changed print statement to raise an exception
Changed overall indentation from 3 spaces to 4
Added pycogent_backports/alpha_diversity.py to incorporate the Gini index, Good's coverage, and the conditional_uncovered_probability.py stuff that was formerly in qiime/qiime. Added the test file as well. Modified All added files to remove redundant imports, a circular import that was causing an error, and changed the distribution of functions in the files to better reflect what each does.
Removed the files which have been incorporated into the backport or alpha_diversity.py
Changed documentation to clarify an explanation
Modified files to update calls so that tests weren't failing.
More modifications to ensure that both scripts/conditional_unocovered_probability.py and scripts/alpha_diversity.py work as expected and each have the correct metrics.
Added table density to per_library_stats.py output.
Merge pull request #522 from jrrideout/issue_232

Added table density to per_library_stats.py output.
Merge pull request #521 from ElDeveloper/issue_145

Resolves issue 145
Modified the documentation of alpha_diversity_metrics.rst to reflect additions.
Merge pull request #520 from ElDeveloper/indentation

Changed overall indentation from 3 spaces to 4
Merge pull request #499 from kpatnode/master

Added Support for Tax2Tree in assign_taxonomy.py